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Phylogeography of Prunus Armeniaca L. by Chloroplast DNA and Nuclear Ribosomal Sequences

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Phylogeography of Prunus Armeniaca L. by Chloroplast DNA and Nuclear Ribosomal Sequences Phylogeography of Prunus Armeniaca L. By Chloroplast DNA and Nuclear Ribosomal Sequences Wen-Wen Li Xinjiang Agricultural University Li-Qiang Liu Xinjiang Agricultural University Qiu-Ping Zhang Liaoning Institute of Pomology Wei-Quan Zhou Xinjiang Agricultural University Guo-Quan Fan Xinjiang Academy of Agricultural Sciences Kang Liao ( [email protected] ) Xinjiang Agricultural University Research Article Keywords: evolutionary history of organisms, P. armeniaca, AMOVA, phytogeography Posted Date: February 22nd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-215210/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Phylogeography of Prunus armeniaca L. by Chloroplast DNA and Nuclear Ribosomal Sequences 1 Wen-Wen Li1, Li-Qiang Liu1, Qiu-Ping Zhang2, Wei-Quan Zhou1, Guo-Quan 2 Fan3, Kang Liao1* 3 1College of Horticulture and Forestry, Xinjiang Agricultural University, Urumqi, Xinjiang, 4 China. 2Xiongyue National Germplasm Resources Garden of the Liaoning Institute of 5 Pomology, Xiongyue, Shenyang, China. 3Luntai National Fruit Germplasm Resources 6 Garden of Xinjiang Academy of Agricultural Sciences, Luntai, Xinjiang, China. email: 7 [email protected] 8 Abstract 9 To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA 10 fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed 11 spacer (ITS) were employed to assess the genetic variation across 12 P. armeniaca 12 populations. The results of cpDNA and ITS sequence data analysis showed that the 13 level of genetic diversity in P. armeniaca was high (cpDNA: HT=0.499; ITS: 14 HT=0.876), and the level of genetic differentiation was low (cpDNA: FST=0.1628; ITS: 15 FST=0.0297). An analysis of molecular variance (AMOVA) revealed that most of the 16 genetic variation in P. armeniaca occurred among individuals within populations. The 17 value of interpopulation differentiation (NST) was significantly higher than the number 18 of substitution types (GST), indicating a genealogical structure in P. armeniaca. P. 19 armeniaca shared the same genotypes with related species and may be associated with 20 them through continuous and extensive gene flow. The haplotypes/genotypes of 21 cultivated apricot populations in Xinjiang, North China, and foreign apricot 22 populations were mixed with large numbers of haplotypes/genotypes of wild apricot 23 populations from the Ili River Valley. The wild apricot populations in the Ili River 24 Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity 25 and were located in an area considered a potential glacial refugiume for P. armeniaca. 26 Since population expansion occurred 16.53 kyr ago, the area has provided a suitable 27 climate for the population and protected the genetic diversity of P. armeniaca. 28 Introduction 29 The evolutionary history of organisms, including their genetic diversity, population 30 structure and historical dynamics, is critical to species conservation 1. Understanding 31 the effects of climate change on the spatial genetic patterns of species, particularly 32 endangered species, can help reveal not only the evolutionary history of species but 33 also conservation strategies 2-3. The origins of mountain biodiversity are complex and 1 34 may include the immigration of preadapted lineages 4-5, in situ diversification 6, or the 35 continuation of ancestral lineages 7. Compared with those of other mountains, such as 36 the Hengduan Mountains, the evolution and diversity of the Tianshan Mountains are 37 still poorly understood. The Ili River Valley is located in the western part of the 38 Tianshan Mountains in China and is surrounded by mountains on three sides. This 39 valley was the main northern crossing of the ancient Silk Road. In the late Tertiary 40 period, a large number of species, including wild apricot, wild apple and wild 41 hawthorn, remained in the Ili River Valley and were important components of the 42 deciduous broad-leaved forest at elevations below the coniferous forest and above the 43 mountain grassland belt in the Xinjiang Uygur Autonomous Region, China 8. 44 However, there are few studies on the phylogeography of plant species in the arid 45 region of Northwest China 9-10. 46 In recent decades, the method of combining molecular data with paleoclimatic and 47 geographical evidence has been effective in the study of system geography 11-12. Many 48 systematic geographic studies have shown that the Last Glacial Maximum (LGM) of 49 the Pleistocene strongly influenced the genetic variation and biodiversity of plants 50 throughout the Northern Hemisphere 13-14. Especially during the Quaternary glacial 51 period, species in the ice-free zone were mainly affected by the cold and dry climate 52 15. Climatic fluctuations cause the distribution of species to shrink and expand 16, and 53 cold and dry climates prompted species to retreat to refugia, providing shelter for 54 plants and animals 17. As temperatures rose after the glacial period, species underwent 55 population expansion, changes that left a genetic signature in their current populations 56 18. Although no unified glacial sheet had occurred in Asia, paleodata suggested that 57 the distribution ranges of woody species in this region were similarly changed by the 58 Quaternary climatic oscillations 19. Based on the geographical distribution of genetic 59 variation, the glacial refuges and postglacial revegetation routes of most woody plants 60 are roughly consistent with fossil evidence 20. However, due to the lack of fossil 61 evidence, genetic evidence has become an important means of providing information 62 on the distribution range of some woody species and the history of glacial refugia 21-22. 63 Volkova 23 interpret the observed genetic structure [nuclear (ITS) and plastid DNA] of 64 the Eurasian populations of Prunus padus as plausibly resulted from at least two 65 cycles of glacial survivals in refugia followed by post-glacial colonization events. 66 17The complex geographic history may have provided a refuge for species from the 67 last glacial period 17. Xu et al. 24 proposed that there were two possible independent 68 glacial refugia in Northwest China: the Ili River Valley and the Northern Junggar 69 Basin. Su et al. 9 speculate that aggravation of the dry and cold climate during the 70 early Quaternary, combined with plant physiological features, were determining 71 factors contributing to the lineage split, and climate oscillations most likely led to the 72 Yili range expansion. Therefore, it is of great interest to study the systematic 73 geography of endemic plants in Northwest China against the background of 74 Quaternary climatic fluctuations. 75 Apricot is a fruit of temperate and subtropical regions. Turkey, Uzbekistan, Iran, 76 Algeria, Italy, Spain, China, Pakistan, France and Japan are the main producers of 2 77 apricots (http://www.fao.org/home/zh). Apricot belongs to the section Armeniaca 78 (Lam.) Koch, subgenus Prunophora Focke and genus Prunus (Rosaceae) 25. Almost 79 all cultivated apricots originated from P. armeniaca 26. In China, wild apricot is 80 distributed in the Ili River Valley (Tianshan Mountain area). The species is also 81 distributed along the Tianshan mountains and westward to Kazakhstan, Kyrgyzstan 82 and Uzbekistan. It is a relic of a broad-leaved forest from the late Tertiary period, 83 which played a decisive role in the domestication of cultivated apricots worldwide 27. 84 As the world experienced extreme weather events, especially glacial periods, and 85 most species went extinct, some of the more complex valleys may have become 86 refugia for surviving forests and locally present species. As a result, traces of the 87 species may be gradually shrinking in such areas. So, is Ili River Valley a glacial 88 refugia for wild apricot? 89 Generally, seed dispersal distance is much less than that of pollen, and population 90 divergence due to genetic drift will be more marked for chloroplast DNA (cpDNA) 91 than for nuclear DNA. Indeed, cpDNA is considered to evolve very slowly, with low 92 recombination and mutation rates 28. Organelle markers could provide powerful tools 93 for studying the phylogeography and migratory footprints of species 29. Parental 94 genetic markers are often combined with single-parent organelle markers for 95 population genetics studies 30. cpDNA and ITS sequence variations have been very 96 effective in revealing the glacial refuges of plants 29. cpDNA lineages usually show 97 the unique geographical distribution and evolutionary history of natural populations 98 and are therefore widely used in studies of systematic geography 31. Li et al. 32 99 successfully used cpDNA and ITS markers to evaluate the diversity and phylogenetic 100 relationships among populations of Saxifraga sinomontana, indicating that the species 101 had microrefugia during the Quaternary glacial period. In this study, we employed 102 cpDNA (trnL-trnF and ycf1) and nuclear ribosomal DNA (nrDNA) sequences to (1) 103 reveal the haplotype/genotypic diversity and population genetic structure of the 104 species; (2) test for potential glacial refugia for the species in the Ili River Valley; and 105 (3) assess whether the refugia show signs of recent expansion. 106 Materials and methods 107 Sample collection 108 The samples used for cpDNA analysis included 123 individuals from 20 populations. 109 A total of 171 individuals from 19 populations was used for the ITS analysis, of 110 which 38 samples were obtained from the NCBI database (Table S1). The samples 111 studied were from P. armeniaca and related species (P. sibirica, NAG; P. 112 mandshurica, LX; P. dasycarpa, ZX; P. mume, ECG; Prunus zhengheensis, ZHX 33; 113 Prunus limeixing, LMX 33 and Prunus brigantina, FGX). Prunus davidiana (T) was 114 regarded as the outgroup. 115 Our collection of wild apricot (P. armeniaca) populations covered most of the 116 natural distribution in China, including Huocheng County (DZGhcmd, DZGhcy and 117 DZGhcm populations), Yining County (DZGyn population), Gongliu County 3 118 (DZGglb and DZGgld populations) and Xinyuan County (DZGxyt, DZGxya and 119 DZGxyz populations).
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